In situ proteolysis for protein crystallization and structure determination

Aiping Dong; Xiaohui Xu; Aled M. Edwards; Changsoo Chang; Maksymilian Chruszcz; Marianne Cuff; Marcin Cymborowski; Rosa Di Leo; Olga Egorova; Elena Evdokimova; Ekaterina Filippova; Jun Gu; Jennifer Guthrie; Alexandr Ignatchenko; Andrzej Joachimiak; Natalie Klostermann; Youngchang Kim; Yuri Korniyenko; Wladek Minor; Qiuni Que; Alexei Savchenko; Tatiana Skarina; Kemin Tan; Alexander Yakunin; Adelinda Yee; Veronica Yim; Rongguang Zhang; Hong Zheng; Masato Akutsu; Cheryl Arrowsmith; George V. Avvakumov; Alexey Bochkarev; Lars Göran Dahlgren; Sirano Dhe-Paganon; Slav Dimov; Ludmila Dombrovski; Patrick Finerty; Susanne Flodin; Alex Flores; Susanne Gräslund; Martin Hammerström; Maria Dolores Herman; Bum Soo Hong; Raymond Hui; Ida Johansson; Yongson Liu; Martina Nilsson; Lyudmila Nedyalkova; Pär Nordlund; Tomas Nyman; Jinrong Min; Hui Ouyang; Hee Won Park; Chao Qi; Wael Rabeh; Limin Shen; Yang Shen; Deepthi Sukumard; Wolfram Tempel; Yufeng Tong; Lionel Tresagues; Masoud Vedadi; John R. Walker; Johan Weigelt; Martin Welin; Hong Wu; Ting Xiao; Hong Zeng; Haizhong Zhu

doi:10.1038/nmeth1118

In situ proteolysis for protein crystallization and structure determination

Aiping Dong, Xiaohui Xu, Aled M. Edwards^*, Changsoo Chang, Maksymilian Chruszcz, Marianne Cuff, Marcin Cymborowski, Rosa Di Leo, Olga Egorova, Elena Evdokimova, Ekaterina Filippova, Jun Gu, Jennifer Guthrie, Alexandr Ignatchenko, Andrzej Joachimiak, Natalie Klostermann, Youngchang Kim, Yuri Korniyenko, Wladek Minor, Qiuni QueAlexei Savchenko, Tatiana Skarina, Kemin Tan, Alexander Yakunin, Adelinda Yee, Veronica Yim, Rongguang Zhang, Hong Zheng, Masato Akutsu, Cheryl Arrowsmith, George V. Avvakumov, Alexey Bochkarev, Lars Göran Dahlgren, Sirano Dhe-Paganon, Slav Dimov, Ludmila Dombrovski, Patrick Finerty, Susanne Flodin, Alex Flores, Susanne Gräslund, Martin Hammerström, Maria Dolores Herman, Bum Soo Hong, Raymond Hui, Ida Johansson, Yongson Liu, Martina Nilsson, Lyudmila Nedyalkova, Pär Nordlund, Tomas Nyman, Jinrong Min, Hui Ouyang, Hee Won Park, Chao Qi, Wael Rabeh, Limin Shen, Yang Shen, Deepthi Sukumard, Wolfram Tempel, Yufeng Tong, Lionel Tresagues, Masoud Vedadi, John R. Walker, Johan Weigelt, Martin Welin, Hong Wu, Ting Xiao, Hong Zeng, Haizhong Zhu

^*Corresponding author for this work

Biochemistry and Molecular Genetics

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Abstract

We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.

Original language	English (US)
Pages (from-to)	1019-1021
Number of pages	3
Journal	Nature Methods
Volume	4
Issue number	12
DOIs	https://doi.org/10.1038/nmeth1118
State	Published - Dec 2007

Funding

This work was supported by US National Institutes of Health grant GM074942, by the US Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357, and by the Structural Genomics Consortium, which is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canadian Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, Karolinska Institutet, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., Inc., the Novartis Research Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research and the Wellcome Trust.

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth1118

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Dong, A., Xu, X., Edwards, A. M., Chang, C., Chruszcz, M., Cuff, M., Cymborowski, M., Di Leo, R., Egorova, O., Evdokimova, E., Filippova, E., Gu, J., Guthrie, J., Ignatchenko, A., Joachimiak, A., Klostermann, N., Kim, Y., Korniyenko, Y., Minor, W., ... Zhu, H. (2007). In situ proteolysis for protein crystallization and structure determination. Nature Methods, 4(12), 1019-1021. https://doi.org/10.1038/nmeth1118

@article{68dff67c1d304fa08738c69a851129ee,

title = "In situ proteolysis for protein crystallization and structure determination",

abstract = "We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.",

author = "Aiping Dong and Xiaohui Xu and Edwards, {Aled M.} and Changsoo Chang and Maksymilian Chruszcz and Marianne Cuff and Marcin Cymborowski and {Di Leo}, Rosa and Olga Egorova and Elena Evdokimova and Ekaterina Filippova and Jun Gu and Jennifer Guthrie and Alexandr Ignatchenko and Andrzej Joachimiak and Natalie Klostermann and Youngchang Kim and Yuri Korniyenko and Wladek Minor and Qiuni Que and Alexei Savchenko and Tatiana Skarina and Kemin Tan and Alexander Yakunin and Adelinda Yee and Veronica Yim and Rongguang Zhang and Hong Zheng and Masato Akutsu and Cheryl Arrowsmith and Avvakumov, {George V.} and Alexey Bochkarev and Dahlgren, {Lars G{\"o}ran} and Sirano Dhe-Paganon and Slav Dimov and Ludmila Dombrovski and Patrick Finerty and Susanne Flodin and Alex Flores and Susanne Gr{\"a}slund and Martin Hammerstr{\"o}m and Herman, {Maria Dolores} and Hong, {Bum Soo} and Raymond Hui and Ida Johansson and Yongson Liu and Martina Nilsson and Lyudmila Nedyalkova and P{\"a}r Nordlund and Tomas Nyman and Jinrong Min and Hui Ouyang and Park, {Hee Won} and Chao Qi and Wael Rabeh and Limin Shen and Yang Shen and Deepthi Sukumard and Wolfram Tempel and Yufeng Tong and Lionel Tresagues and Masoud Vedadi and Walker, {John R.} and Johan Weigelt and Martin Welin and Hong Wu and Ting Xiao and Hong Zeng and Haizhong Zhu",

note = "Funding Information: This work was supported by US National Institutes of Health grant GM074942, by the US Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357, and by the Structural Genomics Consortium, which is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canadian Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, Karolinska Institutet, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., Inc., the Novartis Research Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research and the Wellcome Trust.",

year = "2007",

month = dec,

doi = "10.1038/nmeth1118",

language = "English (US)",

volume = "4",

pages = "1019--1021",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "12",

}

Dong, A, Xu, X, Edwards, AM, Chang, C, Chruszcz, M, Cuff, M, Cymborowski, M, Di Leo, R, Egorova, O, Evdokimova, E, Filippova, E, Gu, J, Guthrie, J, Ignatchenko, A, Joachimiak, A, Klostermann, N, Kim, Y, Korniyenko, Y, Minor, W, Que, Q, Savchenko, A, Skarina, T, Tan, K, Yakunin, A, Yee, A, Yim, V, Zhang, R, Zheng, H, Akutsu, M, Arrowsmith, C, Avvakumov, GV, Bochkarev, A, Dahlgren, LG, Dhe-Paganon, S, Dimov, S, Dombrovski, L, Finerty, P, Flodin, S, Flores, A, Gräslund, S, Hammerström, M, Herman, MD, Hong, BS, Hui, R, Johansson, I, Liu, Y, Nilsson, M, Nedyalkova, L, Nordlund, P, Nyman, T, Min, J, Ouyang, H, Park, HW, Qi, C, Rabeh, W, Shen, L, Shen, Y, Sukumard, D, Tempel, W, Tong, Y, Tresagues, L, Vedadi, M, Walker, JR, Weigelt, J, Welin, M, Wu, H, Xiao, T, Zeng, H & Zhu, H 2007, 'In situ proteolysis for protein crystallization and structure determination', Nature Methods, vol. 4, no. 12, pp. 1019-1021. https://doi.org/10.1038/nmeth1118

TY - JOUR

T1 - In situ proteolysis for protein crystallization and structure determination

AU - Dong, Aiping

AU - Xu, Xiaohui

AU - Edwards, Aled M.

AU - Chang, Changsoo

AU - Chruszcz, Maksymilian

AU - Cuff, Marianne

AU - Cymborowski, Marcin

AU - Di Leo, Rosa

AU - Egorova, Olga

AU - Evdokimova, Elena

AU - Filippova, Ekaterina

AU - Gu, Jun

AU - Guthrie, Jennifer

AU - Ignatchenko, Alexandr

AU - Joachimiak, Andrzej

AU - Klostermann, Natalie

AU - Kim, Youngchang

AU - Korniyenko, Yuri

AU - Minor, Wladek

AU - Que, Qiuni

AU - Savchenko, Alexei

AU - Skarina, Tatiana

AU - Tan, Kemin

AU - Yakunin, Alexander

AU - Yee, Adelinda

AU - Yim, Veronica

AU - Zhang, Rongguang

AU - Zheng, Hong

AU - Akutsu, Masato

AU - Arrowsmith, Cheryl

AU - Avvakumov, George V.

AU - Bochkarev, Alexey

AU - Dahlgren, Lars Göran

AU - Dhe-Paganon, Sirano

AU - Dimov, Slav

AU - Dombrovski, Ludmila

AU - Finerty, Patrick

AU - Flodin, Susanne

AU - Flores, Alex

AU - Gräslund, Susanne

AU - Hammerström, Martin

AU - Herman, Maria Dolores

AU - Hong, Bum Soo

AU - Hui, Raymond

AU - Johansson, Ida

AU - Liu, Yongson

AU - Nilsson, Martina

AU - Nedyalkova, Lyudmila

AU - Nordlund, Pär

AU - Nyman, Tomas

AU - Min, Jinrong

AU - Ouyang, Hui

AU - Park, Hee Won

AU - Qi, Chao

AU - Rabeh, Wael

AU - Shen, Limin

AU - Shen, Yang

AU - Sukumard, Deepthi

AU - Tempel, Wolfram

AU - Tong, Yufeng

AU - Tresagues, Lionel

AU - Vedadi, Masoud

AU - Walker, John R.

AU - Weigelt, Johan

AU - Welin, Martin

AU - Wu, Hong

AU - Xiao, Ting

AU - Zeng, Hong

AU - Zhu, Haizhong

N1 - Funding Information: This work was supported by US National Institutes of Health grant GM074942, by the US Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357, and by the Structural Genomics Consortium, which is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canadian Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, Karolinska Institutet, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., Inc., the Novartis Research Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research and the Wellcome Trust.

PY - 2007/12

Y1 - 2007/12

N2 - We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.

AB - We tested the general applicability of in situ proteolysis to form protein crystals suitable for structure determination by adding a protease (chymotrypsin or trypsin) digestion step to crystallization trials of 55 bacterial and 14 human proteins that had proven recalcitrant to our best efforts at crystallization or structure determination. This is a work in progress; so far we determined structures of 9 bacterial proteins and the human aminoimidazole ribonucleotide synthetase (AIRS) domain.

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UR - http://www.scopus.com/inward/citedby.url?scp=36749034218&partnerID=8YFLogxK

U2 - 10.1038/nmeth1118

DO - 10.1038/nmeth1118

M3 - Article

C2 - 17982461

AN - SCOPUS:36749034218

SN - 1548-7091

VL - 4

SP - 1019

EP - 1021

JO - Nature Methods

JF - Nature Methods

IS - 12

ER -

In situ proteolysis for protein crystallization and structure determination

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